I want some of my vertebrates to have four limbs, and some of them to have six. Is this even possible? Would there be more four limbed creatures, more six limbed, or just an equal amount?
It's possible for some vertebrae to be six-limbed - there's nothing restrictive about being a vertebrae that limits itself to only four limbs. The reason the vast majority of the living vertebrae you see today are four-limbed is generally believed to be because they've all evolved from a common four-limbed ancestor. However, should you wish it, there's nothing stopping you from adding a six-limbed ancestor and additionally populating the world with six-limbed vertebrae.
As for which one would have more members - well, that's largely going to be a tale of 'the early bird gets the worm', as in, the first set of species to evolve within an ecological niche will edge out all other species, so it's really up for grabs as to which has more members unless one of the ancestors shows up a good several hundred thousand years before the other.
The easiest option to achieve that would be to just make all of your animal vertebrate life to descent from the six-limbed ancestor, with some groups of animal lineages losing their third pair of legs for various evolutionary reasons (for example something with an equine-like style of wandering the prairies would probably benefit from ditching a couple of limbs to become more aerodynamic, lightweight and able to run more efficiently with wider strides)